Highly Scalable Genotype Phasing by Entropy Minimization. - Bogdan Pasaniuc; Ion I. Mandoiu (EMBC, 2006)

Genotype Error Detection Using Hidden Markov Models of Haplotype Diversity. - Justin Kennedy; Ion I. Mandoiu; Bogdan Pasaniuc (J. Comput. Biol., 2008)

Highly Scalable Genotype Phasing by Entropy Minimization. - Alexander Gusev; Ion I. Mandoiu; Bogdan Pasaniuc (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

Imputation-Based Local Ancestry Inference in Admixed Populations. - Bogdan Pasaniuc; Justin Kennedy; Ion I. Mandoiu (ISBRA, 2009)

Inference of locus-specific ancestry in closely related populations. - Bogdan Pasaniuc; Sriram Sankararaman; Gad Kimmel; Eran Halperin (Bioinform., 2009)

GEDI: Scalable Algorithms for Genotype Error Detection and Imputation - Justin Kennedy; Ion I. Mandoiu; Bogdan Pasaniuc (CoRR, 2009)

Genotyping common and rare variation using overlapping pool sequencing. - Dan He 001; Noah Zaitlen; Bogdan Pasaniuc; Eleazar Eskin; Eran Halperin (BMC Bioinform., 2011)

Optimal Testing of Digital Microfluidic Biochips. - Bogdan Pasaniuc; Robert S. Garfinkel; Ion I. Mandoiu; Alexander Zelikovsky (INFORMS J. Comput., 2011)

Accurate Estimation of Expression Levels of Homologous Genes in RNA-seq Experiments. - Bogdan Pasaniuc; Noah Zaitlen; Eran Halperin (J. Comput. Biol., 2011)

Fast and accurate inference of local ancestry in Latino populations. - Yael Baran; Bogdan Pasaniuc; Sriram Sankararaman; Dara G. Torgerson; Christopher Gignoux; Celeste Eng; William Rodriguez-Cintron; Rocio Chapela; Jean G. Ford; Pedro C. Avila; Jose Rodriguez-Santana; Esteban Gonzàlez Burchard; et al. (Bioinform., 2012)

Analysis of case-control association studies with known risk variants. - Noah Zaitlen; Bogdan Pasaniuc; Nick Patterson; Samuela Pollack; Benjamin Voight; Leif Groop; David Altshuler; Brian E. Henderson; Laurence N. Kolonel; Loic Le Marchand; Kevin Waters; Christopher A. Haiman; et al. (Bioinform., 2012)

Analysis of Latino populations from GALA and MEC studies reveals genomic loci with biased local ancestry estimation. - Bogdan Pasaniuc; Sriram Sankararaman; Dara G. Torgerson; Christopher Gignoux; Noah Zaitlen; Celeste Eng; William Rodriguez-Cintron; Rocio Chapela; Jean G. Ford; Pedro C. Avila; Jose Rodriguez-Santana; Gary K. Chen; et al. (Bioinform., 2013)

Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data. - Wen-Yun Yang; Farhad Hormozdiari; Zhanyong Wang; Dan He 001; Bogdan Pasaniuc; Eleazar Eskin (Bioinform., 2013)

Identifying causal variants at loci with multiple signals of association. - Farhad Hormozdiari; Emrah Kostem; Eun Yong Kang; Bogdan Pasaniuc; Eleazar Eskin (BCB, 2014)

A Spatial-Aware Haplotype Copying Model with Applications to Genotype Imputation. - Wen-Yun Yang; Farhad Hormozdiari; Eleazar Eskin; Bogdan Pasaniuc (RECOMB, 2014)

Fast and accurate imputation of summary statistics enhances evidence of functional enrichment. - Bogdan Pasaniuc; Noah Zaitlen; Huwenbo Shi; Gaurav Bhatia; Alexander Gusev; Joseph Pickrell; Joel Hirschhorn; David P. Strachan; Nick Patterson; Alkes L. Price (Bioinform., 2014)

Enhanced Methods for Local Ancestry Assignment in Sequenced Admixed Individuals. - Robert Brown; Bogdan Pasaniuc (PLoS Comput. Biol., 2014)

Identification of causal genes for complex traits. - Farhad Hormozdiari; Gleb Kichaev; Wen-Yun Yang; Bogdan Pasaniuc; Eleazar Eskin (Bioinform., 2015)

A multivariate Bernoulli model to predict DNaseI hypersensitivity status from haplotype data. - Huwenbo Shi; Bogdan Pasaniuc; Kenneth L. Lange (Bioinform., 2015)

A Spatial Haplotype Copying Model with Applications to Genotype Imputation. - Wen-Yun Yang; Farhad Hormozdiari; Eleazar Eskin; Bogdan Pasaniuc (J. Comput. Biol., 2015)

Enhanced methods to detect haplotypic effects on gene expression. - Robert Brown; Gleb Kichaev; Nicholas Mancuso; James Boocock; Bogdan Pasaniuc (Bioinform., 2017)

Improved methods for multi-trait fine mapping of pleiotropic risk loci. - Gleb Kichaev; Megan Roytman; Ruth Johnson; Eleazar Eskin; Sara Lindström; Peter Kraft; Bogdan Pasaniuc (Bioinform., 2017)

A Bayesian framework for multiple trait colocalization from summary association statistics. - Claudia Giambartolomei; Jimmy Zhenli Liu; Wen Zhang; Mads Hauberg; Huwenbo Shi; James Boocock; Joe Pickrell; Andrew E. Jaffe; CommonMind Consortium; Bogdan Pasaniuc; Panos Roussos (Bioinform., 2018)

A unifying framework for joint trait analysis under a non-infinitesimal model. - Ruth Johnson; Huwenbo Shi; Bogdan Pasaniuc; Sriram Sankararaman (Bioinform., 2018)

Scalable Multi-component Linear Mixed Models with Application to SNP Heritability Estimation. - Ali Pazokitoroudi; Yue Wu; Kathryn S. Burch; Kangcheng Hou; Bogdan Pasaniuc; Sriram Sankararaman (RECOMB, 2019)

RAISS: robust and accurate imputation from summary statistics. - Hanna Julienne; Huwenbo Shi; Bogdan Pasaniuc; Hugues Aschard (Bioinform., 2019)

Estimating Enzyme Participation in Metabolic Pathways for Microbial Communities from RNA-seq Data. - Filipp Rondel; Akram Sadat Hosseini; Bikram Sahoo; Sergey Knyazev; Igor Mandric; Frank Stewart; Ion I. Mandoiu; Bogdan Pasaniuc; Alex Zelikovsky (ISBRA, 2020)

A Scalable Method for Estimating the Regional Polygenicity of Complex Traits. - Ruth Johnson; Kathryn S. Burch; Kangcheng Hou; Mario Paciuc; Bogdan Pasaniuc; Sriram Sankararaman (RECOMB, 2020)

Integrative Analyses Identify Susceptibility Genes Underlying COVID-19 Hospitalization. - Kritika Singh; Gita Pathak; Tyne Miller-Flemming; Frank Wendt; Nava Ehsan; Kangcheng Hou; Ruth Johnson; Zeyun Lu; Shyamalika Gopalan; Loic Yang; Pejman Mohammadi 001; Bogdan Pasaniuc; et al. (AMIA, 2021)

A two-step approach to testing overall effect of gene-environment interaction for multiple phenotypes. - Arunabha Majumdar; Kathryn S. Burch; Tanushree Haldar; Sriram Sankararaman; Bogdan Pasaniuc; W. James Gauderman; John S. Witte (Bioinform., 2021)

Pipeline for Analyzing Activity of Metabolic Pathways in Planktonic Communities Using Metatranscriptomic Data. - Filipp Rondel; Roya Hosseini; Bikram Sahoo; Sergey Knyazev; Igor Mandric; Frank Stewart; Ion I. Mandoiu; Bogdan Pasaniuc; Yuri Porozov; Alexander Zelikovsky (J. Comput. Biol., 2021)

Estimation of regional polygenicity from GWAS provides insights into the genetic architecture of complex traits. - Ruth Johnson; Kathryn S. Burch; Kangcheng Hou; Mario Paciuc; Bogdan Pasaniuc; Sriram Sankararaman (PLoS Comput. Biol., 2021)

Leveraging eQTLs to identify individual-level tissue of interest for a complex trait. - Arunabha Majumdar; Claudia Giambartolomei; Na Cai; Tanushree Haldar; Tommer Schwarz; Michael J. Gandal; Jonathan Flint; Bogdan Pasaniuc (PLoS Comput. Biol., 2021)

twas_sim, a Python-based tool for simulation and power analysis of transcriptome-wide association analysis. - Xinran Wang; Zeyun Lu; Arjun Bhattacharya; Bogdan Pasaniuc; Nicholas Mancuso (Bioinform., 2023)